SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock

BMC Genomics

Table 1 Consistency of information across SNP chip and assemblies

					rs IDs without map information^e
SNPchip	Total^a	no rs ID^b	rsID ×2^c	rsID ×3^d	BTAU4.2	UMD3.1	BTAU4.6
Bovine3k^f	2,900	14	0	0	17	5	20
BovineLD^g	6,909	3	0	1	94	14	111
BovineSNP50v.1^h	54,001	0	29	0	1,970	204	1,852
BovineSNP50v.2ⁱ	54,609	18	29	0	2,154	340	2,031
BovineHD^j	777,962	13	96	5	72,014	3,338	64,528
Axiom BOS 1^k	648,875	288,601	1	0	130,618	0	16,207

^aTotal number of SNPs/SNP probes within chip not considering cross-references of SNP IDs.
^bTotal number of SNPs without SNP ID – rs ID association.
^cTotal number of SNPs with two different SNP IDs and same rs ID.
^dTotal number of SNPs with three different SNP IDs and same rs ID.
^eTotal number of SNPs whose rs ID is not mapped in the correspondent assembly (coded as chromosome 99 and position 0 in the SNPchiMp database).
^fIllumina Golden Gate Bovine3K BeadChip.
^gIllumina Infinium BovineLD BeadChip.
^hIllumina Infinium BovineSNP50 v.1 BeadChip.
ⁱIllumina Infinium BovineSNP50 v.2 BeadChip.
^jIllumina Infinium BovineHD BeadChip.
^kAffymetrix Axiom Genome-Wide BOS 1.

ISSN: 1471-2164